Amino Acids And Different Functional Groups

Different types of bonds/interactions in proteins lead to different kinds of structures. Three of the most commonly known chemical bonds in proteins include the hydrogen bond, the covalent bond, and the ionic bond. In hydrogen bonds, hydrogen interacts with oxygen, nitrogen, or fluorine to form either the alpha helix, or the beta sheet, which in turn determines its secondary, tertiary, or quaternary structure. Another type of bonds, the covalent bond, links amino acids together by sharing electrons;

Proteins are the basis of the protoplasm (fluid living content of the cell that contains the cytoplasm and cell nucleus) and are found in all living organisms. Proteins make up the bulk of animals body’s non-skeletal structure. As enzymes, they catalyze biochemical reactions; as antibodies, they prevent the effects of invading organisms; and as hormones, they control metabolic processes (C. Bissonnette, 2011). The Biuret test was used to detect the presence of peptide bonds within proteins, and they were found present in test tube #9 (control for peptide bonds).

Proteins are polymers made by joining up small molecules called amino acids. Amino acids and proteins are made mainly of the elements carbon, hydrogen, oxygen and nitrogen.

Box on right illustrates the peptide bond resulting from the condensation of both the amino acids. The box on the left illustrates the separation of the hydroxide group from glycine and the hydrogen atom from valine.

Proteins are complex structures made up of chains of amino acids. Each protein has a different function such as enzymes to catalyze reactions or protein hormones to trigger certain functions of a cell. First let’s start with the most basic component of a protein: an amino acid. An amino acid is made up of a central carbon atom attached to a hydrogen atom, a carboxyl group, an amino group, and an R group which varies

The amino acids bond together in bonds called peptide bonds. A chain of amino acids is called a polypeptide chain. The structure in which the amino acids are bonded determines the function of the protein. There are about twenty different amino acids, but there is a wide variety of possible combinations that amino acids can bond, therefore proteins have quite a lot of functions. Some things proteins are used for are the building of the muscles, tendons, organs, glands, nails, and hair. There are many more different functions for proteins. To detect proteins in test materials, there is an identifying agent called Biuret Solution which when mixed with the test material. It turns purple if it contains a protein. The darker the violet color, the more concentrated it is with protein.

They are made up of amino acids (consists of amino group, carboxyl group, hydrogen atom, and R group). Polypeptide bonds form between amino acids to form polypeptide chains. Amino acid sequence is primary protein structure. The secondary structure is the bonding pattern of the amino acids (e.g. helix, sheet, etc.). The tertiary structure consists of the domain, where the sheets or helixes fold on each other and become stable. The quaternary structure consists of several polypeptide chains that form advanced proteins such as human leukocyte

The structure of an enzyme as protein has a primary, secondary, tertiary, and sometimes quaternary structure. The primary structure of an enzyme, like any protein, is the order of its amino acids. The secondary structure involves alpha helices and beta pleated sheets. Alpha helices are a coil that is formed by hydrogen bonding between every fourth amino acid. Beta pleated sheets are formed by hydrogen bonding between two or more parts of the polypeptide chain that are side by side. The tertiary structure contains disulfide bridges, ionic bonds, hydrophobic interactions, and hydrogen bonds. Disulfide bridges are the result of two sulfhydryl groups interacting because the the folding of the protein. Ionic bonds can form between polar groups on amino acids. Hydrophobic interactions are the cluster of amino acids with nonpolar side chains that is commonly seen in proteins. Hydrogen bonds can also form. The quaternary structure of an enzyme is when multiple proteins are bonded together in one complex made of proteins subunits.

Proteins are polymeric chains that are built from monomers called amino acids. All structural and functional properties of proteins derive from the chemical properties of the polypeptide chain. There are four levels of protein structural organization: primary, secondary, tertiary, and quaternary. Primary structure is defined as the linear sequence of amino acids in a polypeptide chain. The secondary structure refers to certain regular geometric figures of the chain. Tertiary structure results from long-range contacts within the chain. The quaternary structure is the organization of protein subunits, or two or more independent polypeptide chains.

This assignment will outline the function of proteins in living organisms and the important roles of different types of protein. “Protein composes 10-30% of cell mass and is the basic structural material of the body” (Marieb E.N.M et al, 2004). Protein is a nutrient that living organisms need to exist and grow, as well as water being a key feature. “All protein contains carbon, oxygen, hydrogen and nitrogen” (Marieb E.N.M et al, 2004). Amino acids form links of 20, “The sequences at which they are bound together produces proteins that vary widely in both structure and function” (Marieb E.N.M et al, 2004).

We know that proteins are basically just amino acids bonded by peptide bonds which form a chain. However the function of protein is determined by the structure of that protein itself, we can determine the structure of an amino acid by observing what sequence the amino are in, each protein or polypeptide as its own unique sequence of amino acids, we refer

a) The tertiary structure refers to the structural arrangement of amino acids that are found far away from one another along the polypeptide chain. The tertiary structure is overall a three dimensional shape of a protein molecule. It will bend and twist to achieve maximum stability. The shape of a tertiary structure is made when the secondary structure folds in on itself and is held in place by many bonds and interactions formed by the R groups in the amino acid chain. The bonds and interactions involved are hydrogen bonds, ionic bonds, hydrophobic interactions and disulphide bonds. These bonds and interactions are located in different areas of the tertiary structure, the hydrogen bonds are located inbetween polar R groups, ionic bonds are located between charged R groups, hydrophobic interactions are located between nonpolar R groups and disulphide bonds are formed generally in the endoplasmic reticulum by oxidation ."Hydrogen bonds may form between different side­chain groups." Hydrophobic interactions are brought about in an aqueous site. The tertiary structure is held together mainly by interactions that are located at the R groups.

A protein is made from a chain of 20 amino acids, which is called polypeptides. As the biologic workhorses, proteins perform vital functions in every cell.

We have the sequences and the PDB files for all proteins that have been successfully aligned with active peptides. We design self-inhibitory peptides targeting these proteins using SIP. The process consists in four steps that will be briefly described here: The first step is the secondary structure prediction followed by the second step, which is the disorder prediction. These first two steps are based on the protein sequence only. The third step is the selection of segments of 20 amino acid long, with low disorder and helical secondary structure, within the protein. And finally, the fourth step is the calculation of the the energy score based of the structural information from the PDB file.

Campbell and Farrell define proteins as polymers of amino acids that have been covalently joined through peptide bonds to form amino acid chains (61). A short amino acid chain comprising of thirty amino acids forms a peptide, and a longer chain of amino acids forms a polypeptide or a protein. Each of the amino acids making up a protein, has a fundamental design that comprises of a central carbon or alpha carbon that is bonded to a hydrogen element, an amino grouping, a carboxyl grouping, and a unique side chain or the R-group (Campbell and Farrell 61).